[gmx-users] merging chains in gromos43a1p

Justin Lemkul jalemkul at vt.edu
Wed Dec 3 22:55:57 CET 2014

On 12/3/14 4:52 PM, Jayant James wrote:
> Hi!
> I was wondering if there is the -merge option in pdb2gmx in gromacs 4.5.4?
> It some how seems like version 4.5.4 that I have for simulating
> phosphorylated serines does not have this option.
> Since I am trying to simulate a protein that has three chains comprised
> into one protein I normally prefer to number them sequentially. The
> sequential numbering helps in indexing for simulated annealing because it
> is easy to choose the amino acids that I need to heat and cool.

My 43a1p files work with any version from 4.5 onward, so you can (and probably 
should) use a newer Gromacs version.  The "version 4.5" tag just indicates 
that's when the organization of the files changed.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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